KEGG

This MCP server provides comprehensive access to KEGG data via a REST-like interface exposed through the MCP SDK. It aggregates KEGG resources such as pathways, genes, compounds, reactions, diseases, drugs, modules, glycans, and BRITE hierarchies, along with advanced analysis tools for cross-references and identifier conversion. The server exposes a suite of tools grouped into categories (Database Information & Statistics, Pathway Analysis, Gene Analysis, Compound Analysis, Reaction & Enzyme Analysis, Disease & Drug Analysis, Module & Orthology Analysis, Glycan Analysis, BRITE Hierarchy Analysis, Advanced Analysis Tools, and Cross-References & Integration). You can perform operations like searching for pathways or genes, retrieving detailed entry information, converting identifiers between KEGG and external databases, and obtaining pathway components or related entries. Use the templates and resource templates to fetch structured data for downstream analysis in bioinformatics workflows.

Prerequisites:

• Node.js and npm installed on your system
• Git installed for cloning the repository

Installation steps:

1. Clone the server repository: git clone https://github.com/augmented-nature/augmented-nature-kegg-mcp-server.git
2. Navigate to the server directory: cd augmented-nature-kegg-mcp-server
3. Install dependencies: npm install
4. Build the server (if applicable): npm run build
5. Start the server (development or production): npm start // or run the built entry if a specific script is provided, e.g., node dist/server.js

Note: The project uses the MCP SDK. If you prefer running via npx, you can also start with: npx -y augmented-nature-kegg-mcp-server

Tips and common considerations:

• Ensure your environment has network access to KEGG REST endpoints; some environments may require proxy configuration.
• The server supports batch and streaming-style requests; use batch_entry_lookup for processing multiple KEGG entries efficiently.
• If you encounter timeouts, adjust timeout settings where supported by the MCP SDK or implement client-side retries with backoff.
• Review the API coverage to understand which KEGG resources are exposed (INFO, LIST, FIND, GET, CONV, LINK) and how to format parameters for each tool.
• Enable caching where appropriate to improve performance for frequently requested entries.
• Check environment variables for API keys or rate-limiting controls if the deployment environment requires them.
• When upgrading, consult the CHANGELOG or Version History for breaking changes in tool availability or data formats.